Commented the function spam.label.fixUndersegmentation() and respective test

tests/test_label.py

@@ -501,53 +501,53 @@ class TestFunctionLabel(unittest.TestCase):
         res = spam.label.label.Spheroid(10, 20, dim = 3).digitize()
         self.assertIsNotNone(res)
 
-    def _test_FixUnderSegmentation(self):
-        # Generate two prolate grains (rice-like)
-        grain1 = spam.label.label.Spheroid(10, 20, numpy.asarray([0,1,0])).digitize()
-        grain2 = spam.label.label.Spheroid(10, 20, numpy.asarray([0,1,0])).digitize()
-        # Create the bigger  labelled image
-        grainIm = numpy.concatenate((grain1,grain2))
-        grainIm = numpy.zeros(grainIm.shape)
-        # Add the grains to the bigger image
-        grainIm[:grain1.shape[0]-1,:,:] = grain1[:grain1.shape[0]-1,:,:]
-        grainIm[grain2.shape[0]-5:-5,:,:] =  grainIm[grain2.shape[0]-5:-5,:,:] + grain1[:,:,:]
-        # Set all the labels to 1
-        grainIm = numpy.where(grainIm >= 1, 3, grainIm)
-        # Pad a border
-        grainIm = numpy.pad(grainIm, pad_width=10, mode='constant', constant_values = 0)
-        # Create the 'greyScale' image
-        greyIm = numpy.where(grainIm == 3, 30000, 10000)
-
-        # Check that the greyscale image is normalized
-        res1 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.5, 20*0.5)
-        self.assertEqual(res1, None)
-        # Check that a or c is valid
-        res2 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], numpy.nan, numpy.nan)
-        self.assertEqual(res2, None)
-        # Check that a or c are positive
-        res3 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], -1, 10)
-        self.assertEqual(res3, None)
-
-        # Run fixUnderSegmentation
-        greyIm = numpy.where(grainIm == 3, 0.75, 0.25)
-        res4 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, vect = [[0,1,0]])
-        # Check that there are two grains
-        self.assertEqual(numpy.max(numpy.unique(res4)), 2)
-        # Check that it runs even if the label does not exist
-        res5 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, vect = [[0,1,0]])
-        self.assertIsNotNone(res5)
-        # Check for a vect that is not a list
-        res6 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, vect = (0,1,0))
-        self.assertIsNone(res6)
-        # Check that it works without the input vect
-        res7 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, numVect = 1)
-        self.assertIsNotNone(res7)
-        # Check that it works with verbose = True
-        res8 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, numVect = 1, verbose = True)
-        self.assertIsNotNone(res8)
-        # Check that it works even for a non-existing label
-        res9 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [5], 10*0.8, 20*0.8, numVect = 1)
-        self.assertIsNotNone(res9)
+    #def test_FixUnderSegmentation(self):
+        #Generate two prolate grains (rice-like)
+        #grain1 = spam.label.label.Spheroid(10, 20, numpy.asarray([0,1,0])).digitize()
+        #grain2 = spam.label.label.Spheroid(10, 20, numpy.asarray([0,1,0])).digitize()
+        #Create the bigger  labelled image
+        #grainIm = numpy.concatenate((grain1,grain2))
+        #grainIm = numpy.zeros(grainIm.shape)
+        #Add the grains to the bigger image
+        #grainIm[:grain1.shape[0]-1,:,:] = grain1[:grain1.shape[0]-1,:,:]
+        #grainIm[grain2.shape[0]-5:-5,:,:] =  grainIm[grain2.shape[0]-5:-5,:,:] + grain1[:,:,:]
+        #Set all the labels to 1
+        #grainIm = numpy.where(grainIm >= 1, 3, grainIm)
+        #Pad a border
+        #grainIm = numpy.pad(grainIm, pad_width=10, mode='constant', constant_values = 0)
+        #Create the 'greyScale' image
+        #greyIm = numpy.where(grainIm == 3, 30000, 10000)
+
+        #Check that the greyscale image is normalized
+        #res1 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.5, 20*0.5)
+        #self.assertEqual(res1, None)
+        #Check that a or c is valid
+        #res2 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], numpy.nan, numpy.nan)
+        #self.assertEqual(res2, None)
+        #Check that a or c are positive
+        #res3 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], -1, 10)
+        #self.assertEqual(res3, None)
+
+        #Run fixUnderSegmentation
+        #greyIm = numpy.where(grainIm == 3, 0.75, 0.25)
+        #res4 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, vect = [[0,1,0]])
+        #Check that there are two grains
+        #self.assertEqual(numpy.max(numpy.unique(res4)), 2)
+        #Check that it runs even if the label does not exist
+        #res5 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, vect = [[0,1,0]])
+        #self.assertIsNotNone(res5)
+        #Check for a vect that is not a list
+        #res6 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, vect = (0,1,0))
+        #self.assertIsNone(res6)
+        #Check that it works without the input vect
+        #res7 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, numVect = 1)
+        #self.assertIsNotNone(res7)
+        #Check that it works with verbose = True
+        #res8 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [3], 10*0.8, 20*0.8, numVect = 1, verbose = True)
+        #self.assertIsNotNone(res8)
+        #Check that it works even for a non-existing label
+        #res9 = spam.label.label.fixUndersegmentation(grainIm, greyIm, [5], 10*0.8, 20*0.8, numVect = 1)
+        #self.assertIsNotNone(res9)
         
 
     def test_contactOrientations(self):
@@ -709,6 +709,32 @@ class TestFunctionLabel(unittest.TestCase):
         imLab2 = spam.label.moveLabels(imLab, PhiField, boundingBoxes = boundingBoxes, centresOfMass = centresOfMass)
         self.assertIsNotNone(imLab2)
         
+        # Test 7 -> Check that it runs for more than one grain....
+        # Create two grains
+        grain1 = spam.label.label.Spheroid(15, 15, numpy.asarray([0,1,0])).digitize()
+        grain1 = numpy.pad(grain1, (5), 'constant', constant_values=(0))
+        grain1 = numpy.where(grain1, 1, 0)
+        grain2 = spam.label.label.Spheroid(15, 15, numpy.asarray([0,1,0])).digitize()
+        grain2 = numpy.pad(grain2, (5), 'constant', constant_values=(0))
+        grain2 = numpy.where(grain2, 2, 0)
+        grainIm = numpy.concatenate((grain1,grain2))
+        grainIm = numpy.zeros(grainIm.shape)
+        grainIm[:grain1.shape[0]-1,:,:] = grain1[:grain1.shape[0]-1,:,:]
+        grainIm[grain2.shape[0]-5:-5,:,:] =  grainIm[grain2.shape[0]-5:-5,:,:] + grain2[:,:,:]
+        grainIm = grainIm.astype(int)
+        # Create empty PhiField
+        PhiField = numpy.zeros((3, 4, 4))
+        # Compute initial volume & COM
+        COM = spam.label.centresOfMass(grainIm)
+        iniVol = spam.label.volumes(grainIm)
+        # Apply a displacement
+        transformation = {'t': [1, 1, 1]}
+        PhiField[1] = spam.deformation.computePhi(transformation)
+        transformation = {'t': [-1, -1, -1]}
+        PhiField[2] = spam.deformation.computePhi(transformation)
+        imLab2 = spam.label.moveLabels(grainIm, PhiField)
+        self.assertIsNotNone(imLab2)
+        
     def test_erodeLabels(self):
         # Create the sphere
         imLab = skimage.morphology.ball(20)